Banding Techniques Method by itskimo
Guide Matching and Hand Banding Techniques '"Home" and "Q" keys ' At the start of a new game the beginning state of the protein is centered in the frame along with the gray guide. If you don't see them hit "Home" or "Q" keys to recenter the view. As a protein is disturbed by a tug or a script, the backbone changes shape, wiggles and turns all about. This at times causes the protein to travel away from the center of the frame. The gray guide can be turned on/off in View menu. 'The Guide' The guide appears as a shadow of the known position of the protein in its most favored, relaxed, highest scoring state. Matching the guide is a technique which is useful to beginners to learn in that it will help in mastery of many of the tools and techniques of folding. It will also give some experience in what well folded proteins might look like and how they might behave. This is a discussion on the use of some of those tools and techniques on how to match the protein to the guide. Once the guide drifts away from the protein, it is best to realign the guide to a central part of the protein, right click to select center guide, and then band the backbone to the guide, starting near the center. Then wiggle shake etc Keep repeating . As you do this it brings the backbone closer and closer to the guide. 'Unbanding and Stablizing' Finaly, when you are ready to unband, freeze the tips or end loops of the backbone by wheel-clicking on the selected segments of the protein. This is to keep it from flying apart when you delete the bands, and w s w again. At this point you can also unfreeze and run "Stabilize" and wswssw again if you think the protein is solid enough that it won't come apart. If at anytime your protein does explode or otherwise drops off the chart, STOP ASAP! Then restore or undo to a good spot and try again. Then realign the guide again. Band and do it all over again. Then re-band wsw, freeze tips, delete bands wws, unfreeze stabilize wsw, re-align , and do it again and again until you get close to matching the guide. 'Banding the Sidechains' Once the backbone is close to being in place, You can then band the sidechains along with the backbone. This helps to better align the backbone. When you start on the sidechains,changing to stick + proton view and zoom in real close. Then band down the protons to the guide. The side chain guides well pop up gray when you pass over the side chains. By banding the sidechains it helps to twist the backbone closer to the guide. Also keep sheets banded or freeze good spots on the backbone to keep them from shifting. Then its, wsw, freeze tips delete bands, wsw unfreeze, stabilize, wsw if you think the protein is stable enough to stay together wsw etc, and then start all over again. 'Why this helps' Every protein backbone shape has a specific static resting state depending on its side chain bonds that it settles into. When pulling with rubber bands the protein shifts and rotates, bonds change, let the movement of the protein be your guide, GO WITH IT!. Try to help the protein go the way it wants to move. Like an old house in a hurricane, when the wind blows, every joint moves, a push here, a change there, the doors rattle and the windows shake. What we are trying to do is push that old protein back up again after the windstorm, to stand straight once again, upright, and tall, and just like a house of cards, your protein can collapse in a pile at the slightest push or pull in the wrong direction, especially when it is not secured by bands or frozen segments. By re-aligning re-banding recentering etc This banding, pull, relax, and re-banding allows the protein's evolving structure to settle, and lets the changing protein hopefully align closer to the guide. 'Using different views can really help ' For working on the backbone the cartoon view with outlines & white background is clearer. When doing sidechains try using the proton & stick view and zoom way in. Wsw or swws or wwsww or whatever = wiggle & shake or any other combination for any duration you think is right. More Techniques at > The Foldit Labs Category:Itskimo strategy